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Updated: Feb 21, 2026
A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors
Published on: April 29, 2022
Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics
Sohrab Saraei1, Tomi Suomi1, Otto Kauko1
1Bioinformatics Unit, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland.
Motivation:
Global centering-based normalization is a commonly used normalization approach in mass spectrometry-based label-free proteomics. It scales the peptide abundances to have the same median intensities, based on an assumption that the majority of abundances remain the same across the samples. However, especially in phosphoproteomics, this assumption can introduce bias, as the samples are enriched during sample preparation which can mask the underlying biological changes. To address this possible bias, phosphopeptides quantified in both enriched and non-enriched samples can be used to calculate factors that mitigate the bias.
Results:
We present an R package phosphonormalizer for normalizing enriched samples in label-free mass spectrometry-based phosphoproteomics.
Availability And Implementation:
The phosphonormalizer package is freely available under GPL ( > =2) license from Bioconductor (https://bioconductor.org/packages/phosphonormalizer).
Contact:
sohrab.saraei@utu.fi or laura.elo@utu.fi.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
